View Vacancy -- PhD Student - MGU 551
The MRC Harwell Institute and Oxford Big Data Institute (BDI), University of Oxford, are offering two PhD studentships for collaborative projects between the two institutes. The students will benefit from being located at the BDI, while spending two days per week at the MRC Harwell Institute and will be jointly supervised by a supervisor from each institution. These collaborative studentships will offer potential to leverage some of the large multidimensional data analysis challenges that span both institutes and allow the extensive mouse functional datasets curated at the MRC Harwell Institute to be aligned to the large collection of population data at the BDI.
The MRC Harwell Institute is a world leader in large scale functional studies, including the International Mouse Phenotyping Consortium (IMPC) and is the NIH funded Data Coordination Centre for the IMPC, collecting and analysing data from 10 centres around the world. The BDI is a major international institute established to focus on the collection, integration and analysis of biomedical big data.
Students can select from the projects below and should outline in their covering letter their interest and experience relevant to this project(s).
1. Multivariate analysis of large scale mouse phenotyping data from the IMPC with the UK BioBank data to study the pleiotropic genotype-phenotype relationships. Supervisors: Cecilia Lindgren (BDI) and Ann-Marie Mallon (MRC Harwell Institute)
The IMPC and UK BioBank data resources are large multi-dimensional datasets that comprise of complex biomedical data. Bringing together the large population study from the UK Biobank with the deep based phenotypic data from mouse knockouts in the IMPC, will allow unprecedented opportunities for understanding the mechanisms in an array of disease areas. The pleiotropic effect of many genes remains largely poorly understood as many studies focus on a single disease or endophenotype domain. Both of these datasets, will enable us to look at pleiotropy in granular detail. In addition, the deep multivariate analysis of these datasets together will enable us to dissect complex determinants of disease such as environmental and social interactions. The PhD project will focus on the development of data models and statistical methodologies to analyse the common phenotypic domains, including a focus on comparative image analysis.
2. Understanding the genetic determinants of mammalian behaviour through video capture and statistical machine learning analysis. Supervisors: Chris Holmes (BDI) and Ann-Marie Mallon (MRC Harwell Institute)
This project will investigate new statistical machine learning (ML) methods for video tracking and analysis of animal activity, delivering a step-change for scientists studying the genetic mechanisms of mammalian behaviour utilising the creation of the world’s largest knowledge bank of annotated mouse activity. The MRC Harwell Institute has been at the forefront of developing novel home-cage monitoring systems that allows for 24/7 monitoring of multiple mice in the home cage, delivering insights into the genetics of locomotion, sleep-wake cycle and social interactions. With support from software engineers at Harwell the studentship will explore novel ML methods for a data warehouse built on over 50,000 hours of long term video capture on 750 mice linked with diverse genetic and multivariate phenotype data. The studentship will investigate models for semi-supervised activity labelling of video data using bespoke statistical ML algorithms and novel visualization methods. The project benefits from interaction with leading academics in behavioural mouse genetics, mouse phenotyping, bioinformatics, data visualization, biostatistics, and machine learning.
3. Cross Species Comparison of genome annotation datasets in the functional characterization of metabolic non-coding variation. Supervisors: Cecilia Lindgren (BDI) and Roger Cox (MRC Harwell)
This work will take large population genetic association data sets for metabolic traits and pair this with extensive functional annotation data sets (open chromatin, regulatory chromatin marks, DNA conformation, methylation marks, transcription factor binding sites, expression data etc.) to identify likely causal variants. Subsequently, to manipulate these largely non-coding variants in the mouse for functional and mechanistic analysis requires the mapping of these putative regulatory marks and elements onto the mouse genome to identify equivalent regions. There are publicly available mouse ‘omics’ data sets and we have started to generate our own specialised data sets in specific tissues and cells. For example, we now have ATAC-seq data from differentiating mouse stromal vascular fraction derived adipocytes from visceral and subcutaneous depots and are starting to generate similar sets for human cells and tissues. The next steps are to comparatively map signals between mouse and human in metabolically important cells and tissues. We will then manipulate these in vitro and in vivo in mouse to look at phenotypic consequences. The PhD project will focus on ‘big data’ analysis in human metabolic disease paired with mouse functional genetics to exploit the unprecedented opportunities to mechanistically understand determinants.
Students are registered with the University of Oxford and the relevant department who will award the DPhil/PhD. The studentship includes an annual stipend of £15,240 and University and college fees for students meeting the UK residence requirements detailed on the MRC Harwell Institute website careers pages (https://www.har.mrc.ac.uk/careers).
The MRC studentships, provides students with a stipend and also pay PhD/DPhil registration fees at the University of Oxford. This funding is only available to candidates that meet the UK residence criteria as detailed in the Research Council UK (RCUK) conditions of research council training grants.
To be eligible for a full award (stipend and university fees) a student must have:
- Settled status in the UK, meaning they have no restrictions on how long they can stay.
- Been ‘ordinarily resident’ in the UK for three years prior to the start of the studentship. This means they must have been normally residing in the UK (apart from temporary or occasional absences).
- Not been residing in the UK wholly or mainly for the purpose of full-time education. (This does not apply to UK or EU nationals).
Choosing to come to work at the MRC (part of UKRI) means that you will have access to a whole host of benefits from a defined benefit pension scheme and excellent holiday entitlement to access to employee shopping/travel discounts and salary sacrifice cycle to work scheme, as well as the chance to put the MRC and UKRI on your CV in the future.
Our success is dependent upon our ability to embrace diversity and draw on the skills, understanding and experience of all our people. We welcome applications from all sections of the community irrespective of gender, race, ethnic or national origin, religion or belief, sexual orientation, disability or age. As "Disability Confident" employers, we guarantee to interview all applicants with disabilities who meet the minimum criteria for the vacancy.
UKRI supports research in areas that include animal health, agriculture and food security, and bioscience for health which includes research on animals, genetic modification and stem cell research. Whilst you may not have direct involvement in this type of research, you should consider whether this conflicts with your personal values or beliefs.
We will conduct a full and comprehensive pre-employment check as an essential part of the recruitment process on all individuals that are offered a position with UKRI. This will include a security check and an extreme organisations affiliation check.
This opportunity is closed to applications.